+Open data
-Basic information
Entry | Database: PDB / ID: 6m4j | ||||||
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Title | SspA in complex with cysteine | ||||||
Components | SspA complex protein | ||||||
Keywords | OXIDOREDUCTASE / cysteine desulfhydrase | ||||||
Function / homology | Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / 3-Layer(aba) Sandwich / Alpha Beta / CYSTEINE / PYRIDOXAL-5'-PHOSPHATE Function and homology information | ||||||
Biological species | Vibrio cyclitrophicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Liu, L. / Gao, H. | ||||||
Citation | Journal: Mbio / Year: 2020 Title: Structural Analysis of an l-Cysteine Desulfurase from an Ssp DNA Phosphorothioation System. Authors: Liu, L. / Jiang, S. / Xing, M. / Chen, C. / Lai, C. / Li, N. / Liu, G. / Wu, D. / Gao, H. / Hong, L. / Tan, P. / Chen, S. / Deng, Z. / Wu, G. / Wang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m4j.cif.gz | 313.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m4j.ent.gz | 254.8 KB | Display | PDB format |
PDBx/mmJSON format | 6m4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/6m4j ftp://data.pdbj.org/pub/pdb/validation_reports/m4/6m4j | HTTPS FTP |
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-Related structure data
Related structure data | 3vaxS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 37897.465 Da / Num. of mol.: 2 / Mutation: C314S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cyclitrophicus (bacteria) / Production host: Escherichia coli (E. coli) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Sequence details | The sequence has been deposited to NCBI with accession code WP_016789103.1. And C314S mutation was introduced. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.05 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.8M ammonium citrate, pH 7.0 / PH range: 6.5-7.5 |
-Data collection
Diffraction | Mean temperature: 173 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 1, 2016 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→115 Å / Num. obs: 72776 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.962 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 1.8→1.84 Å / Num. unique obs: 11922 / CC1/2: 0.962 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VAX Resolution: 1.8→114.54 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.106 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.106 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.79 Å2 / Biso mean: 22.156 Å2 / Biso min: 12.27 Å2
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Refinement step | Cycle: final / Resolution: 1.8→114.54 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 537 / Type: TIGHT THERMAL / Rms dev position: 3.24 Å / Weight position: 0.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.801→1.848 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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